rs1555967

Variant names:

• chr6-51295197-G-A
• rs1555967

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.216 in 152,070 control chromosomes in the GnomAD database, including 3,880 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.22 (3880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32787 AN: 151952 Hom.: 3884 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.192

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.216 AC: 32796 AN: 152070 Hom.: 3880 Cov.: 32 AF XY: 0.220 AC XY: 16362 AN XY: 74324

African (AFR) AF: 0.138 AC: 5725 AN: 41512

American (AMR) AF: 0.327 AC: 4989 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 747 AN: 3472

East Asian (EAS) AF: 0.191 AC: 982 AN: 5148

South Asian (SAS) AF: 0.314 AC: 1517 AN: 4824

European-Finnish (FIN) AF: 0.248 AC: 2620 AN: 10564

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.229 AC: 15558 AN: 67980

Other (OTH) AF: 0.191 AC: 403 AN: 2114

Alfa AF: 0.213 Hom.: 2398

Bravo AF: 0.215

Asia WGS AF: 0.240 AC: 830 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.32
DANN	Benign	0.35
PhyloP100		-0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1555967; hg19: chr6-51159995;